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Ewing sarcoma (EwS) is characterized by EWSR1-ETS fusion transcription factors converting polymorphic GGAA microsatellites (mSats) into potent neo-enhancers. Although the paucity of additional mutations makes EwS a genuine model to study principles of cooperation between dominant fusion oncogenes and neo-enhancers, this is impeded by the limited number of well-characterized models. Here we present the Ewing Sarcoma Cell Line Atlas (ESCLA), comprising whole-genome, DNA methylation, transcriptome, proteome, and chromatin immunoprecipitation sequencing (ChIP-seq) data of 18 cell lines with inducible EWSR1-ETS knockdown. The ESCLA shows hundreds of EWSR1-ETS-targets, the nature of EWSR1-ETS-preferred GGAA mSats, and putative indirect modes of EWSR1-ETS-mediated gene regulation, converging in the duality of a specific but plastic EwS signature. We identify heterogeneously regulated EWSR1-ETS-targets as potential prognostic EwS biomarkers. Our freely available ESCLA (http://r2platform.com/escla/) is a rich resource for EwS research and highlights the power of comprehensive datasets to unravel principles of heterogeneous gene regulation by chimeric transcription factors.
Pubmed ID: 36476851 RIS Download
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Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.
View all literature mentionsA Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)
View all literature mentionsA software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)
View all literature mentionsOriginal SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsSoftware package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed.
View all literature mentionsA powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
View all literature mentionsSoftware tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
View all literature mentionsVisualize and analyze data generated by all of Illumina''s platforms.
View all literature mentionsAdjusting batch effects in microarray expression data using Empirical Bayes methods.
View all literature mentionsA software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
View all literature mentionsAn efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)
View all literature mentionsSoftware tools for analyzing and visualizing Illumina''s 450k array data.
View all literature mentionsCommercial provider of equipment and resources for epigenetics research, biological sample preparation, and diagnostic assays. The products Diagenode provides include automation and semi-automation software, antibodies, reagents, kits, and shearing technologies.
View all literature mentionsThis unknown targets anti Rabbit IgG (H+L chain)
View all literature mentionsThis polyclonal targets IgG (H+L)
View all literature mentionsThis monoclonal targets FLI-1
View all literature mentionsThis monoclonal targets GAPDH (6C5)
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis monoclonal targets B MyB (phospho T487)
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis polyclonal targets H3K4me3
View all literature mentionsThis polyclonal targets H3K27me3
View all literature mentionsThis polyclonal targets H3K27ac
View all literature mentionsThis polyclonal targets FLI1 antibody - ChIP Grade
View all literature mentions
Mus musculus with name NOD.Cg-Prkdcscid Il2rg
Cell line HEK293T is a Transformed cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line TC-71 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line TC-32 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line TC-106 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line SK-N-MC is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line SK-ES-1 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line EW-8 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line RD-ES is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line POE is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line MIC is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line MHH-ES-1 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line EW-7 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line EW-3 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line EW-24 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line EW-22 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line EW-1 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line CHLA-25 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line CHLA-10 is a Cancer cell line with a species of origin Homo sapiens (Human)
View all literature mentionsCell line A-673 is a Cancer cell line with a species of origin Homo sapiens (Human)
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